Short answer: Atheist.
Long answer: Americans will elect women, more non-Whites, and Jewish people before an atheist or a Muslim is elected.
The Republican party in its current form will never put a non-Christian up as its candidate. Christianity is absolutely the base for Republican beliefs. So the Atheists and Muslims will have to duke it out within 3rd parties and the Democratic party. So we will never see a big showdown between an Atheist and a Muslim in the final presidential election.
Despite the fact that in 2006 Atheists were voted to be least trusted (source), I think the xenophobes in America are more afraid of Muslims. It seems that they think all terrorists are Muslims, and all Muslims are friends with one-another, so any Muslim candidate also has beers with Saddam on Friday nights, plotting world domination.
Meanwhile, they may think Atheism is laughable, or that it’s even unamerican, I don’t think they are afraid of Atheists being terrorists.
Terrorism is a pretty hot issue these days.